4JV5

Crystal structures of pseudouridinilated stop codons with ASLs

> Summary

Summary for 4JV5

DescriptorPROTEIN/RNA Complex
Functional Keywords30s ribosomal particle, protein synthesis, ribosome
Biological sourceThermus thermophilus
More
Total number of polymer chains23
Total molecular weight769608.96
Authors
Fernandez, I.S.,Ng, C.L.,Kelley, A.C.,Guowei, W.,Yu, Y.T.,Ramakrishnan, V. (deposition date: 2013-03-25, release date: 2013-06-26, modification date: 2013-08-21)
Primary citation
Fernandez, I.S.,Ng, C.L.,Kelley, A.C.,Wu, G.,Yu, Y.T.,Ramakrishnan, V.
Unusual base pairing during the decoding of a stop codon by the ribosome.
Nature, 500:107-110, 2013
PubMed: 23812587
DOI: 10.1038/nature12302
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (3.162 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliersRNA backbone0.247166.7%20.1%1.4%0.36MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 4jv5
no rotation
Molmil generated image of 4jv5
rotated about x axis by 90°
Molmil generated image of 4jv5
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A16S ribosomal RNApolymer1517492373.71
GenBank (AP008226.1)
Thermus thermophilus
B30S ribosomal protein S2polymer23426987.51
UniProt (P80371)
Pfam (PF00318)
Thermus thermophilus
C30S ribosomal protein S3polymer20622862.61
UniProt (P80372)
Pfam (PF00189)
Pfam (PF07650)
Thermus thermophilus
D30S ribosomal protein S4polymer20824242.41
UniProt (P80373)
Pfam (PF00163)
Pfam (PF01479)
Thermus thermophilus
E30S ribosomal protein S5polymer15016331.21
UniProt (Q5SHQ5)
Pfam (PF00333)
Pfam (PF03719)
Thermus thermophilus
F30S ribosomal protein S6polymer10111988.91
UniProt (Q5SLP8)
Pfam (PF01250)
Thermus thermophilus
G30S ribosomal protein S7polymer15517919.91
UniProt (P17291)
Pfam (PF00177)
Thermus thermophilus
H30S ribosomal protein S8polymer13815868.71
UniProt (Q5SHQ2)
Pfam (PF00410)
Thermus thermophilus
I30S ribosomal protein S9polymer12714298.61
UniProt (P80374)
Pfam (PF00380)
Thermus thermophilus
J30S ribosomal protein S10polymer9811299.31
UniProt (Q5SHN7)
Pfam (PF00338)
Thermus thermophilus
K30S ribosomal protein S11polymer11912606.51
UniProt (P80376)
Pfam (PF00411)
Thermus thermophilus
L30S ribosomal protein S12polymer12513875.51
UniProt (Q5SHN3)
Pfam (PF00164)
Thermus thermophilus
M30S ribosomal protein S13polymer12013624.01
UniProt (P80377)
Pfam (PF00416)
Thermus thermophilus
N30S ribosomal protein S14polymer607027.61
UniProt (Q5SHQ1)
Pfam (PF00253)
Thermus thermophilus
O30S ribosomal protein S15polymer8810447.31
UniProt (Q5SJ76)
Pfam (PF00312)
Thermus thermophilus
P30S ribosomal protein S16polymer839924.61
UniProt (Q5SJH3)
Pfam (PF00886)
Thermus thermophilus
Q30S ribosomal protein S17polymer9911723.01
UniProt (Q5SHP7)
Pfam (PF00366)
Thermus thermophilus
R30S ribosomal protein S18polymer708155.91
UniProt (Q5SLQ0)
Pfam (PF01084)
Thermus thermophilus
S30S ribosomal protein S19polymer788949.51
UniProt (Q5SHP2)
Pfam (PF00203)
Thermus thermophilus
T30S ribosomal protein 20polymer9910921.21
UniProt (P80380)
Pfam (PF01649)
Thermus thermophilus
U30S ribosomal protein THXpolymer242960.51
UniProt (Q5SIH3)
Pfam (PF17070)
Thermus thermophilus
XmRNApolymer51571.01
Synthetic construct
YASL-tRNApolymer103171.01
Synthetic construct
MAGNESIUM IONnon-polymer24.317
ZINC IONnon-polymer65.41

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains23
Total molecular weight769130.4
Non-Polymers*Number of molecules18
Total molecular weight478.6
All*Total molecular weight769609.0
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (3.162 Å)

Cell axes401.000401.000176.000
Cell angles90.0090.0090.00
SpacegroupP 41 21 2
Resolution limits29.88 - 3.16
the highest resolution shell value3.243 - 3.162
R-factor0.20002
R-work0.19744
the highest resolution shell value0.313
R-free0.24905
the highest resolution shell value0.345
RMSD bond length0.009
RMSD bond angle1.698

Data Collection Statistics

Resolution limits45.80 - 3.10
the highest resolution shell value -
Number of reflections241499
Completeness99.2
the highest resolution shell value2.9
I/sigma(I)1

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1EVAPORATION6.5277.15

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
J0005840cellular_componentribosome
J0019843molecular_functionrRNA binding
J0003735molecular_functionstructural constituent of ribosome
J0000049molecular_functiontRNA binding
J0006412biological_processtranslation
K0005840cellular_componentribosome
K0019843molecular_functionrRNA binding
K0003735molecular_functionstructural constituent of ribosome
K0006412biological_processtranslation
L0015935cellular_componentsmall ribosomal subunit
L0019843molecular_functionrRNA binding
L0003735molecular_functionstructural constituent of ribosome
L0000049molecular_functiontRNA binding
L0006412biological_processtranslation
M0005840cellular_componentribosome
M0019843molecular_functionrRNA binding
M0003735molecular_functionstructural constituent of ribosome
M0000049molecular_functiontRNA binding
M0006412biological_processtranslation
N0005840cellular_componentribosome
N0019843molecular_functionrRNA binding
N0003735molecular_functionstructural constituent of ribosome
N0008270molecular_functionzinc ion binding
N0006412biological_processtranslation
O0005840cellular_componentribosome
O0019843molecular_functionrRNA binding
O0003735molecular_functionstructural constituent of ribosome
O0006412biological_processtranslation
P0005840cellular_componentribosome
P0003735molecular_functionstructural constituent of ribosome
P0006412biological_processtranslation
Q0005840cellular_componentribosome
Q0019843molecular_functionrRNA binding
Q0003735molecular_functionstructural constituent of ribosome
Q0006412biological_processtranslation
R0005840cellular_componentribosome
R0019843molecular_functionrRNA binding
R0003735molecular_functionstructural constituent of ribosome
R0006412biological_processtranslation
S0015935cellular_componentsmall ribosomal subunit
S0019843molecular_functionrRNA binding
S0003735molecular_functionstructural constituent of ribosome
S0006412biological_processtranslation
T0005840cellular_componentribosome
T0019843molecular_functionrRNA binding
T0003735molecular_functionstructural constituent of ribosome
T0006412biological_processtranslation
B0015935cellular_componentsmall ribosomal subunit
B0019843molecular_functionrRNA binding
B0003735molecular_functionstructural constituent of ribosome
B0006412biological_processtranslation
C0015935cellular_componentsmall ribosomal subunit
C0003729molecular_functionmRNA binding
C0019843molecular_functionrRNA binding
C0003735molecular_functionstructural constituent of ribosome
C0006412biological_processtranslation
D0015935cellular_componentsmall ribosomal subunit
D0046872molecular_functionmetal ion binding
D0019843molecular_functionrRNA binding
D0003735molecular_functionstructural constituent of ribosome
D0006412biological_processtranslation
E0015935cellular_componentsmall ribosomal subunit
E0019843molecular_functionrRNA binding
E0003735molecular_functionstructural constituent of ribosome
E0006412biological_processtranslation
F0005840cellular_componentribosome
F0019843molecular_functionrRNA binding
F0003735molecular_functionstructural constituent of ribosome
F0006412biological_processtranslation
G0015935cellular_componentsmall ribosomal subunit
G0019843molecular_functionrRNA binding
G0003735molecular_functionstructural constituent of ribosome
G0000049molecular_functiontRNA binding
G0006412biological_processtranslation
H0005840cellular_componentribosome
H0019843molecular_functionrRNA binding
H0003735molecular_functionstructural constituent of ribosome
H0006412biological_processtranslation
I0005840cellular_componentribosome
I0019843molecular_functionrRNA binding
I0003735molecular_functionstructural constituent of ribosome
I0000049molecular_functiontRNA binding
I0006412biological_processtranslation
U0005840cellular_componentribosome
U0019843molecular_functionrRNA binding
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC14BINDING SITE FOR RESIDUE MG A 1601
ChainResidue
AG1401
AC1402
XPSU4
XA5

AC23BINDING SITE FOR RESIDUE MG A 1603
ChainResidue
AU14
AG15
AA16

AC31BINDING SITE FOR RESIDUE MG A 1604
ChainResidue
AA768

AC42BINDING SITE FOR RESIDUE MG A 1605
ChainResidue
AG581
AG758

AC51BINDING SITE FOR RESIDUE MG A 1606
ChainResidue
AG286

AC62BINDING SITE FOR RESIDUE MG A 1607
ChainResidue
AG576
AC578

AC71BINDING SITE FOR RESIDUE MG A 1608
ChainResidue
AC536

AC81BINDING SITE FOR RESIDUE MG A 1610
ChainResidue
AU560

AC91BINDING SITE FOR RESIDUE MG A 1611
ChainResidue
AG903

BC12BINDING SITE FOR RESIDUE MG A 1613
ChainResidue
AC962
AC1200

BC23BINDING SITE FOR RESIDUE MG A 1614
ChainResidue
AA865
AC866
AG1079

BC31BINDING SITE FOR RESIDUE MG A 1615
ChainResidue
AG1224

BC45BINDING SITE FOR RESIDUE ZN D 301
ChainResidue
DCYS9
DCYS12
DCYS26
DCYS31
DALA32

BC54BINDING SITE FOR RESIDUE MG X 101
ChainResidue
AC518
AG530
LPRO48
XG6

BC62BINDING SITE FOR RESIDUE MG Y 101
ChainResidue
XG6
YI34

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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